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Fang H, Dickey B, PerezLaguna D, Ulloa JV, PerezSanchez P, Xu J. Acidothermus cellulolyticus E1 endoglucanase expressed in planta undergoes extensive hydroxyproline-O-glycosylation and exhibits enhanced impact on biomass digestibility. PLANT CELL REPORTS 2024; 43:202. [PMID: 39073636 DOI: 10.1007/s00299-024-03291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
KEY MESSAGE E1 holoenzyme was extensively Hyp-O-glycosylated at the proline rich linker region in plants, which substantially increased the molecular size and improved the enzymatic digestibility of the biomass of transgenic plants. Thermophilic E1 endo-1,4-β-glucanase derived from Acidothermus cellulolyticus has been frequently expressed in planta to reconstruct the plant cell wall to overcome biomass recalcitrance. However, the expressed holoenzyme exhibited a larger molecular size (~ 100 kDa) than the theoretical one (57 kDa), possibly due to posttranslational modifications in the recombinant enzyme within plant cells. This study investigates the glycosylation of the E1 holoenzyme expressed in tobacco plants and determines its impact on enzyme activity and biomass digestibility. The E1 holoenzyme, E1 catalytic domain (E1cd) and E1 linker (E1Lk) were each expressed in tobacco plants and suspension cells. The accumulation of holoenzyme was 2.0- to 2.3- times higher than that of E1cd. The proline-rich E1Lk region was extensively hydroxyproline-O-glycosylated with arabinogalactan polysaccharides. Compared with E1cd, the holoenzyme displayed a broader optimal temperature range (70 to 85 ºC). When grown in greenhouse, the expression of E1 holoenzyme induced notable phenotypic changes in plants, including delayed flowering and leaf variegation post-flowering. However, the final yield of plant biomass was not significantly affected. Finally, plant biomass engineering with E1 holoenzyme showed 1.7- to 1.8-fold higher saccharification efficiency than the E1cd lines and 2.4- to 2.7-fold higher than the wild-type lines, which was ascribed to the synergetic action of the E1Lk and cellulose binding module in reducing cell wall recalcitrance.
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Affiliation(s)
- Hong Fang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA
- College of Agriculture, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Berry Dickey
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Daniela PerezLaguna
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | | | - Paula PerezSanchez
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72401, USA
| | - Jianfeng Xu
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, 72401, USA.
- College of Agriculture, Arkansas State University, Jonesboro, AR, 72401, USA.
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2
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Zhang G, Liu P, Zhang G, Yao X, Wang X, Zhang Y, Lin J, Cui Y, Li X. Cell wall remodeling promotes callus formation in poplar. MOLECULAR HORTICULTURE 2024; 4:16. [PMID: 38685126 PMCID: PMC11059702 DOI: 10.1186/s43897-024-00093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Geng Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Peipei Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Guifang Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xiaomin Yao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Xinwei Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Yueqian Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Cui
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaojuan Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 10083, China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
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3
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Sharma N, Agarwal A, Bijoy A, Pandit S, Sharma RK. Lignocellulolytic extremozymes and their biotechnological applications. Extremophiles 2023; 28:2. [PMID: 37950773 DOI: 10.1007/s00792-023-01314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.
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Affiliation(s)
- Nikita Sharma
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Aditi Agarwal
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Ananya Bijoy
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Sunidhi Pandit
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Rakesh Kumar Sharma
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India.
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4
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Wu X, Zhao S, Tian Z, Han C, Jiang X, Wang L. Dynamics of loops surrounding the active site architecture in GH5_2 subfamily TfCel5A for cellulose degradation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:154. [PMID: 37853500 PMCID: PMC10583438 DOI: 10.1186/s13068-023-02411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant natural biomass resource for the production of biofuels and other chemicals. The efficient degradation of cellulose by cellulases is a critical step for the lignocellulose bioconversion. Understanding the structure-catalysis relationship is vital for rational design of more stable and highly active enzymes. Glycoside hydrolase (GH) family 5 is the largest and most functionally diverse group of cellulases, with a conserved TIM barrel structure. The important roles of the various loop regions of GH5 enzymes in catalysis, however, remain poorly understood. RESULTS In the present study, we investigated the relationship between the loops surrounding active site architecture and its catalytic efficiency, taking TfCel5A, an enzyme from GH5_2 subfamily of Thermobifida fusca, as an example. Large-scale computational simulations and site-directed mutagenesis experiments revealed that three loops (loop 8, 3, and 7) around active cleft played diverse roles in substrate binding, intermediate formation, and product release, respectively. The highly flexible and charged residue triad of loop 8 was responsible for capturing the ligand into the active cleft. Severe fluctuation of loop 3 led to the distortion of sugar conformation at the - 1 subsite. The wobble of loop 7 might facilitate product release, and the enzyme activity of the mutant Y361W in loop 7 was increased by approximately 40%. CONCLUSION This study unraveled the vital roles of loops in active site architecture and provided new insights into the catalytic mechanism of the GH5_2 cellulases.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhennan Tian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chao Han
- Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Kumari S, Leon Magdaleno JS, Grewal RK, Narsing Rao MP, Rajjak Shaikh A, Cavallo L, Chawla M, Kumar M. High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics. J Biomol Struct Dyn 2023:1-12. [PMID: 37768075 DOI: 10.1080/07391102.2023.2262600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Jorge S Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manoj Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
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6
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Dixit M, Shukla P. Analysis of endoglucanases production using metatranscriptomics and proteomics approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:211-231. [PMID: 38220425 DOI: 10.1016/bs.apcsb.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The cellulases are among the most used enzyme in industries for various purposes. They add up to the green economy perspective and cost-effective production of enterprises. Biorefineries, paper industries, and textile industries are foremost in their usage. The production of endoglucanases from microorganisms is a valuable resource and can be exploited with the help of biotechnology. The present review provides some insight into the uses of endoglucanases in different industries and the potent fungal source of these enzymes. The advances in the enzyme technology has helped towards understanding some pathways to increase the production of industrial enzymes from microorganisms. The proteomics analysis and systems biology tools also help to identify these pathways for the enhanced production of such enzymes. This review deciphers the use of proteomics tools to analyze the potent microorganisms and identify suitable culture conditions to increase the output of endoglucanases. The review also includes the role of quantitative proteomics which is a powerful technique to get results faster and more timely. The role of metatranscriptomic approaches are also described which are helpful in the enzyme engineering for their efficient use under industrial conditions. Conclusively, this review helps to understand the challenges faced in the industrial use of endoglucanases and their further improvement.
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Affiliation(s)
- Mandeep Dixit
- Department of Botany, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
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7
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Biochemical Characterization of an Endoglucanase GH7 from Thermophile Thermothielavioides terrestris Expressed on Aspergillus nidulans. Catalysts 2023. [DOI: 10.3390/catal13030582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Endoglucanases (EC 3.2.1.4) are important enzymes involved in the hydrolysis of cellulose, acting randomly in the β-1,4-glycosidic bonds present in the amorphous regions of the polysaccharide chain. These biocatalysts have been classified into 14 glycosyl hydrolase (GH) families. The GH7 family is of particular interest since it may act on a broad range of substrates, including cellulose, β-glucan, and xylan, an attractive feature for biotechnological applications, especially in the renewable energy field. In the current work, a gene from the thermophilic fungus Thermothielavioides terrestris, encoding an endoglucanase GH7 (TtCel7B), was cloned in the secretion vector pEXPYR and transformed into the high-protein-producing strain Aspergillus nidulans A773. Purified TtCel7B has a molecular weight of approximately 66 kDa, evidenced by SDS-PAGE. Circular dichroism confirmed the high β-strand content consistent with the canonical GH7 family β-jellyroll fold, also observed in the 3D homology model of TtCel7B. Biochemical characterization assays showed that TtCel7B was active over a wide range of pH values (3.5–7.0) and temperatures (45–70 °C), with the highest activity at pH 4.0 and 65 °C. TtCel7B also was stable over a wide range of pH values (3.5–9.0), maintaining more than 80% of its activity after 24 h. The KM and Vmax values in low-viscosity carboxymethylcellulose were 9.3 mg mL−1 and 2.5 × 104 U mg−1, respectively. The results obtained in this work provide a basis for the development of applications of recombinant TtCel7B in the renewable energy field.
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8
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Kumar Saini J, Himanshu, Hemansi, Kaur A, Mathur A. Strategies to enhance enzymatic hydrolysis of lignocellulosic biomass for biorefinery applications: A review. BIORESOURCE TECHNOLOGY 2022; 360:127517. [PMID: 35772718 DOI: 10.1016/j.biortech.2022.127517] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Global interest in lignocellulosic biorefineries has increased in the recent past due to technological advancements in sustainable and cost-effective production of numerous commodity and speciality chemicals and fuels from renewable lignocellulosic biomass (LCB). As a result, the market value of biorefinery products has also increased over the time, with an estimated worth of USD 867.7 billion by 2025. However, biorefinery operations, especially enzymatic hydrolysis, suffer from many challenges that limits the cost-effectiveness of conversion of LCB. Therefore, it is essential to understand and address these challenges in future biorefineries. The paper focuses on recent trends and challenges in enzymatic hydrolysis of LCB during lignocellulosic biorefinery operation for greener synthesis of energy, fuels, chemicals and other high-value products. Insights into the gaps in knowledge and technological challenges have also been addressed together with focus on future research needs and perspectives of enzymatic hydrolysis of LCB for biorefinery applications.
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Affiliation(s)
- Jitendra Kumar Saini
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India.
| | - Himanshu
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Hemansi
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Research & Development Office, Ashoka University, Sonipat, Haryana PIN- 131029, India
| | - Amanjot Kaur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Aayush Mathur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
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9
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Immobilization of endoglucanase isolated from symbiotic bacterium Bacillus safensis CF99 on magnetic nanoparticles. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Biodegradation of Polymers Used in Oil and Gas Operations: Towards Enzyme Biotechnology Development and Field Application. Polymers (Basel) 2022; 14:polym14091871. [PMID: 35567040 PMCID: PMC9100872 DOI: 10.3390/polym14091871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
Linear and crosslinked polymers are commonly used in the oil and gas industry. Guar-derived polymers have been extensively utilized in hydraulic fracturing processes, and recently polyacrylamide and cellulose-based polymers have also found utility. As these polymers are used during various phases of the hydraulic fracturing process, they can accumulate at formation fracture faces, resulting in undesired filter cakes that impede oil and gas recovery. Although acids and chemical oxidizers are often added in the fracturing fluids to degrade or ‘break’ polymer filter cakes, the constant use of these chemicals can be hazardous and can result in formation damage and corrosion of infrastructure. Alternately, the use of enzymes is an attractive and environmentally friendly technology that can be used to treat polymer accumulations. While guar-linkage-specific enzyme breakers isolated from bacteria have been shown to successfully cleave guar-based polymers and decrease their molecular weight and viscosity at reservoir conditions, new enzymes that target a broader range of polymers currently used in hydraulic fracturing operations still require research and development for effective application. This review article describes the current state-of-knowledge on the mechanisms and enzymes involved in biodegradation of guar gum, polyacrylamide (and hydrolyzed polyacrylamide), and carboxymethyl cellulose polymers. In addition, advantages and challenges in the development and application of enzyme breaker technologies are discussed.
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11
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Corrêa TLR, Román EKB, da Silva Cassoli J, dos Santos LV, Pereira GAG. Secretome analysis of Trichoderma reesei RUT-C30 and Penicillium oxalicum reveals their synergic potential to deconstruct sugarcane and energy cane biomasses. Microbiol Res 2022; 260:127017. [DOI: 10.1016/j.micres.2022.127017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/18/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
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12
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Cutolo E, Tosoni M, Barera S, Herrera-Estrella L, Dall'Osto L, Bassi R. A chimeric hydrolase-PTXD transgene enables chloroplast-based heterologous protein expression and non-sterile cultivation of Chlamydomonas reinhardtii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Amin K, Tranchimand S, Benvegnu T, Abdel-Razzak Z, Chamieh H. Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology. Biomolecules 2021; 11:1557. [PMID: 34827555 PMCID: PMC8615776 DOI: 10.3390/biom11111557] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/09/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.
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Affiliation(s)
- Khadija Amin
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Sylvain Tranchimand
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Thierry Benvegnu
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Ziad Abdel-Razzak
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
| | - Hala Chamieh
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
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14
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Bertacchi S, Jayaprakash P, Morrissey JP, Branduardi P. Interdependence between lignocellulosic biomasses, enzymatic hydrolysis and yeast cell factories in biorefineries. Microb Biotechnol 2021; 15:985-995. [PMID: 34289233 PMCID: PMC8913906 DOI: 10.1111/1751-7915.13886] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/30/2022] Open
Abstract
Biorefineries have a pivotal role in the bioeconomy scenario for the transition from fossil‐based processes towards more sustainable ones relying on renewable resources. Lignocellulose is a prominent feedstock since its abundance and relatively low cost. Microorganisms are often protagonists of biorefineries, as they contribute both to the enzymatic degradation of lignocellulose complex polymers and to the fermentative conversion of the hydrolyzed biomasses into fine and bulk chemicals. Enzymes have therefore become crucial for the development of sustainable biorefineries, being able to provide nutrients to cells from lignocellulose. Enzymatic hydrolysis can be performed by a portfolio of natural enzymes that degrade lignocellulose, often combined into cocktails. As enzymes can be deployed in different operative settings, such as separate hydrolysis and fermentation (SHF) or simultaneous saccharification and fermentation (SSF), their characteristics need to be combined with microbial ones to maximize the process. We therefore reviewed how the optimization of lignocellulose enzymatic hydrolysis can ameliorate bioethanol production when Saccharomyces cerevisiae is used as cell factory. Expanding beyond biofuels, enzymatic cocktail optimization can also be pivotal to unlock the potential of non‐Saccharomyces yeasts, which, thanks to broader substrate utilization, inhibitor resistance and peculiar metabolism, can widen the array of feedstocks and products of biorefineries.
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Affiliation(s)
- Stefano Bertacchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Pooja Jayaprakash
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy.,School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, T12 K8AF, Ireland
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, T12 K8AF, Ireland
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
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15
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Navone L, Vogl T, Luangthongkam P, Blinco JA, Luna-Flores CH, Chen X, von Hellens J, Mahler S, Speight R. Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:80. [PMID: 33789740 PMCID: PMC8010977 DOI: 10.1186/s13068-021-01936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/20/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market. RESULTS In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in kcat and KM for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme. CONCLUSIONS Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.
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Affiliation(s)
- Laura Navone
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Jo-Anne Blinco
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Carlos H Luna-Flores
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- Bioproton Pty Ltd, Brisbane, QLD, Australia
| | | | | | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Robert Speight
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
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16
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Mat Razali N, Hisham SN, Kumar IS, Shukla RN, Lee M, Abu Bakar MF, Nadarajah K. Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani. Int J Mol Sci 2021; 22:ijms22042183. [PMID: 33671736 PMCID: PMC7926851 DOI: 10.3390/ijms22042183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.
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Affiliation(s)
- Nurhani Mat Razali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Siti Norvahida Hisham
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Ilakiya Sharanee Kumar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Rohit Nandan Shukla
- Bionivid Technology Pte Ltd., 209, 4th Cross Rd, B Channasandra, East of NGEF Layout, Kasturi Nagar, Bengaluru 560043, Karnataka, India;
| | - Melvin Lee
- Codon Genomics Sdn. Bhd., No 26, Jalan Dutamas 7 Taman Dutamas Balakong, Seri Kembangan 43200, Selangor, Malaysia;
| | | | - Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
- Correspondence:
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17
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Ghosh S, Godoy L, Anchang KY, Achilonu CC, Gryzenhout M. Fungal Cellulases: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Fang H, Hood EE. An Arabinoxylan Extracted from Corn Grain Is Inhibitory to Cellulase Activity. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2020.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hong Fang
- Molecular Biosciences Graduate Program, Arkansas State University, Jonesboro, AR, USA
| | - Elizabeth E. Hood
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
- College of Agriculture, Arkansas State University, Jonesboro, AR, USA
- Infinite Enzymes, LLC, Jonesboro, AR, USA
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19
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Han C, Liu Y, Liu M, Wang S, Wang Q. Improving the thermostability of a thermostable endoglucanase from Chaetomium thermophilum by engineering the conserved noncatalytic residue and N-glycosylation site. Int J Biol Macromol 2020; 164:3361-3368. [PMID: 32888988 DOI: 10.1016/j.ijbiomac.2020.08.225] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/15/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022]
Abstract
Endoglucanases provide an attractive avenue for the bioconversion of lignocellulosic materials into fermentable sugars to supply cellulosic feedstock for biofuels and other value-added chemicals. Thermostable endoglucanases with high catalytic activity are preferred in practical processes. To improve the thermostability and activity of the thermostable β-1,4-endoglucanase CTendo45 isolated from the thermophilic fungus Chaetomium thermophilum, structure-based rational design was performed by using site-directed mutagenesis. When inactivated mutation of the unique N-glycosylation sequon (N88-E89-T90) was implemented and the conserved Y173 residue was substituted with phenylalanine, a double mutant T90A/Y173F demonstrated enzymatic activity that dramatically increased 2.12- and 1.82-fold towards CMC-Na and β-D-glucan, respectively. Additionally, T90A/Y173F exhibited extraordinary heat endurance after 300 min of incubation at elevated temperatures. This study provides a valid approach to the improvement of enzyme redesign protocols and the properties of this endoglucanase mutant distinguish it as an excellent candidate enzyme for industrial biomass conversion.
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Affiliation(s)
- Chao Han
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yifan Liu
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mengyu Liu
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Siqi Wang
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qunqing Wang
- Shandong Key Laboratory for Agricultural Microbiology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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20
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Zhou HY, Zhou JB, Yi XN, Wang YM, Xue YP, Chen DS, Cheng XP, Li M, Wang HY, Chen KQ, Liu ZQ, Zheng YG. Heterologous expression and biochemical characterization of a thermostable endo-β-1,4-glucanase from Colletotrichum orchidophilum. Bioprocess Biosyst Eng 2020; 44:67-79. [PMID: 32772153 DOI: 10.1007/s00449-020-02420-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/29/2020] [Indexed: 01/23/2023]
Abstract
To develop new cellulases for efficient utilization of the lignocellulose, an endoglucanase (CoCel5A) gene from Colletotrichum orchidophilum was synthesized and a recombinant Pichia pastoris GS115/pPIC9K/cocel5A was constructed for secretory expression of CoCel5A. After purification, the protein CoCel5A was biochemically characterized. The endoglucanase CoCel5A exhibited the optimal activity at 55-75 °C and high thermostability (about 85% residual activity) at the temperature of 55 °C after incubation for 3 h. The highest activity of CoCel5A was detected when 100 mM citric acid buffer (pH 4.0-5.0) was used and excellent pH stability (up to 95% residual activity) was observed after incubation in 100 mM citric acid buffer (pH 3.0-6.0) at 4 °C for 24 h. Carboxymethyl cellulose sodium salt (n = approx. 500) (CMC) and β-D-glucan were the best substrates for CoCel5A among the tested substrates. The kinetic parameters Vmax, Km, and Kcat/Km values against CMC were 290.70 U/mg, 2.65 mg/mL, and 75.67 mL/mg/s, respectively; and 228.31 U/mg, 2.06 mg/mL, and 76.45 mL/mg/s against β-D-glucan, respectively, suggesting that CoCel5A has high affinity and catalytic efficiency. These properties supported the potential application of CoCel5A in biotechnological and environmental fields.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jian-Bao Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Nan Yi
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yan-Mei Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - De-Shui Chen
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Xin-Ping Cheng
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Hong-Yan Wang
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Kai-Qian Chen
- Zhejiang Huakang Pharmaceutical Co., LTD, 18 Huagong Road, Huabu Town, Kaihua, 324302, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local, Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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21
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Fang H, Wright T, Jinn JR, Guo W, Zhang N, Wang X, Wang YJ, Xu J. Engineering hydroxyproline-O-glycosylated biopolymers to reconstruct the plant cell wall for improved biomass processability. Biotechnol Bioeng 2020; 117:945-958. [PMID: 31930479 DOI: 10.1002/bit.27266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/23/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022]
Abstract
Reconstructing the chemical and structural characteristics of the plant cell wall represents a promising solution to overcoming lignocellulosic biomass recalcitrance to biochemical deconstruction. This study aims to leverage hydroxyproline (Hyp)-O-glycosylation, a process unique to plant cell wall glycoproteins, as an innovative technology for de novo design and engineering in planta of Hyp-O-glycosylated biopolymers (HypGP) that facilitate plant cell wall reconstruction. HypGP consisting of 18 tandem repeats of "Ser-Hyp-Hyp-Hyp-Hyp" motif or (SP4)18 was designed and engineered into tobacco plants as a fusion peptide with either a reporter protein enhanced green fluorescence protein or the catalytic domain of a thermophilic E1 endoglucanase (E1cd) from Acidothermus cellulolyticus. The engineered (SP4)18 module was extensively Hyp-O-glycosylated with arabino-oligosaccharides, which facilitated the deposition of the fused protein/enzyme in the cell wall matrix and improved the accumulation of the protein/enzyme in planta by 1.5-11-fold. The enzyme activity of the recombinant E1cd was not affected by the fused (SP4)18 module, showing an optimal temperature of 80°C and optimal pH between 5 and 8. The plant biomass engineered with the (SP4)18 -tagged protein/enzyme increased the biomass saccharification efficiency by up to 3.5-fold without having adverse impact on the plant growth.
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Affiliation(s)
- Hong Fang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas
- College of Agriculture, Arkansas State University, Jonesboro, Arkansas
| | - Tristen Wright
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas
| | - Jia-Rong Jinn
- Department of Food Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Wenzheng Guo
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas
| | - Ningning Zhang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas
| | - Xiaoting Wang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas
| | - Ya-Jane Wang
- Department of Food Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Jianfeng Xu
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas
- College of Agriculture, Arkansas State University, Jonesboro, Arkansas
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22
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Oni OD, Oke MA, Sani A. Mixing of Prosopis africana pods and corn cob exerts contrasting effects on the production and quality of Bacillus thuringiensis crude endoglucanase. Prep Biochem Biotechnol 2020; 50:735-744. [PMID: 32129150 DOI: 10.1080/10826068.2020.1734939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Recently, attention has shifted to the use of mixed lignocellulosic substrates for the production of cellulolytic enzymes. However, researchers have focused mainly on achieving increased enzyme yields while neglecting other properties of the enzymes when using such mixtures. In this first-ever report of the application of Prosopis africana pod (PAP) in cellulase production, we investigated the effect of its combination with corn cob (CC), as an inducing carbon source, on the amounts and quality of crude endoglucanase produced by Bacillus thuringiensis SS12. The organism was grown on PAP, CC or their 1:1% w/w mixture (MS) and the crude endoglucanases produced were tested for activity, hydrolytic efficiency, and thermostability. PAP supported the highest enzyme activity (0.138 U/mL) and its endoglucanase was the most effective in hydrolyzing CMC and filter paper while CC-derived endoglucanase was the best for hydrolysis of alkali-pretreated CC. Enzyme activity of MS-derived endoglucanase (0.110 U/mL) was intermediate to that of PAP and CC (0.091 U/mL) and was the most stable at elevated temperatures (70 and 80 °C). It also liberated the least amount of reducing sugars from all tested substrates. Combination of both the substrates, thus, favored enzyme production and thermostability but was detrimental to hydrolytic efficiency.
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Affiliation(s)
- Oyewole Daniel Oni
- Faculty of Life Sciences, Department of Microbiology, University of Ilorin, Ilorin, Nigeria
| | - Mushafau Adebayo Oke
- Department of Biological Sciences Technology, Laboratory Research and Biotechnology, School of Applied Sciences and Technology, Northern Alberta Institute of Technology, Edmonton, Canada
| | - Alhassan Sani
- Faculty of Life Sciences, Department of Microbiology, University of Ilorin, Ilorin, Nigeria
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23
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Han C, Wang Q, Sun Y, Yang R, Liu M, Wang S, Liu Y, Zhou L, Li D. Improvement of the catalytic activity and thermostability of a hyperthermostable endoglucanase by optimizing N-glycosylation sites. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:30. [PMID: 32127917 PMCID: PMC7045587 DOI: 10.1186/s13068-020-1668-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Endoglucanase has been extensively employed in industrial processes as a key biocatalyst for lignocellulosic biomass degradation. Thermostable endoglucanases with high catalytic activity at elevated temperatures are preferred in industrial use. To improve the activity and thermostability, site-directed mutagenesis was conducted to modify the N-glycosylation sites of the thermostable β-1,4-endoglucanase CTendo45 from Chaetomium thermophilum. RESULTS In this study, structure-based rational design was performed based on the modification of N-glycosylation sites in CTendo45. Eight single mutants and one double mutant were constructed and successfully expressed in Pichia pastoris. When the unique N-glycosylation site of N88 was eliminated, a T90A variant was active, and its specific activity towards CMC-Na and β-d-glucan was increased 1.85- and 1.64-fold, respectively. The mutant R67S with an additional N-glycosylation site of N65 showed a distinct enhancement in catalytic efficiency. Moreover, T90A and R67S were endowed with extraordinary heat endurance after 200 min of incubation at different temperatures ranging from 30 to 90 °C. Likewise, the half-lives (t 1/2) indicated that T90A and R67S exhibited improved enzyme thermostability at 80 °C and 90 °C. Notably, the double-mutant T90A/R67S possessed better hydrolysis activity and thermal stability than its single-mutant counterparts and the wild type. CONCLUSIONS This study provides initial insight into the biochemical function of N-glycosylation in thermostable endoglucanases. Moreover, the design approach to the optimization of N-glycosylation sites presents an effective and feasible strategy to improve enzymatic activity and thermostability.
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Affiliation(s)
- Chao Han
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Qunqing Wang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yanxu Sun
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Ruirui Yang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Mengyu Liu
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Siqi Wang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yifan Liu
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Lifan Zhou
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Duochuan Li
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
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Thakur N, Sharma N, Kumar V, Bhalla TC. Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190718150627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Amidases are ubiquitous enzymes and biological functions of these enzymes
vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of
carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals
synthesis, pharmaceuticals agrochemicals and wastewater treatments.
Methods:
They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides,
arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic
site and preferred substrate. Despite their economic importance, we lack knowledge as to how these
amidases withstand elevated pH and temperature whereas others cannot.
Results:
The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant
and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic
organisms revealed some striking trends as to how amino acid composition varies significantly.
Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of
these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L)
in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant
and alkali tolerant amidases.
Conclusion:
The present investigation insights physiochemical properties and dominance of some crucial
amino acid residues in the primary and secondary structure of some amidases from acid-tolerant,
alkali tolerant and neutrophilic microorganisms.
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Affiliation(s)
- Neerja Thakur
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Nikhil Sharma
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
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Molecular simulation of PcCel45A protein expressed from Aspergillus nidulans to understand its structure, dynamics, and thermostability. J Mol Model 2019; 25:317. [PMID: 31598788 DOI: 10.1007/s00894-019-4175-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/19/2019] [Indexed: 10/25/2022]
Abstract
PACS and mathematical subject classification numbers as needed. Molecular dynamic simulation is a very usable tool to understand various factors, including structure temperature dependence, dynamics, and stability for protein structure. The three main components, namely endoglucanase, exoglucanase, and β-glucosidase, effectively convert lignocellulosic biomass into fermentable sugar. Cellulose is the major component of plant cell walls and is the most abundant organic compound on the earth. Somewhat organisms can use cellulose as a food source, possessing cellulases (cellobiohydrolases and endoglucanases) that can catalyze the hydrolysis of the β-(1,4) glycosidic bonds. In this work, we investigated conformational and structural properties of PcCel45A protein by changing at temperatures with 300 K, 333 K, and 352 K. We found that the ASN92 residue was the major contributor to the stability of structure; some other residues correlated significantly with thermal stability. We also compared the theoretical results of the current study with the experimental ones published in previous studies.
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Wuyts S, Allonsius CN, Wittouck S, Thys S, Lievens B, Weckx S, De Vuyst L, Sarah L. Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group. Microb Genom 2019; 5. [PMID: 31368886 PMCID: PMC6807380 DOI: 10.1099/mgen.0.000286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.
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Affiliation(s)
- Sander Wuyts
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Antwerp Centre for Advanced Microscopy (ACAM), University of Antwerp, Antwerp, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lebeer Sarah
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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Nath P, Dhillon A, Kumar K, Sharma K, Jamaldheen SB, Moholkar VS, Goyal A. Development of bi-functional chimeric enzyme (CtGH1-L1-CtGH5-F194A) from endoglucanase (CtGH5) mutant F194A and β-1,4-glucosidase (CtGH1) from Clostridium thermocellum with enhanced activity and structural integrity. BIORESOURCE TECHNOLOGY 2019; 282:494-501. [PMID: 30897487 DOI: 10.1016/j.biortech.2019.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
Site-directed mutagenesis of β-1,4-endoglucanase from family 5 glycoside hydrolase (CtGH5) from Clostridium thermocellum was performed to develop a mutant CtGH5-F194A that gave 40 U/mg specific activity against carboxymethyl cellulose, resulting 2-fold higher activity than wild-type CtGH5. CtGH5-F194A was fused with a β-1,4-glucosidase, CtGH1 from Clostridium thermocellum to develop a chimeric enzyme. The chimera (CtGH1-L1-CtGH5-F194A) expressed as a soluble protein using E. coli BL-21cells displaying 3- to 5-fold higher catalytic efficiency for endoglucanase and β-glucosidase activities. TLC analysis of hydrolysed product of CMC by chimera 1 revealed glucose as final product confirming both β-1,4-endoglucanase and β-1,4-glucosidase activities, while the products of CtGH5-F194A were cellobiose and cello-oligosaccharides. Protein melting studies of CtGH5-F194A showed melting temperature (Tm), 68 °C and of CtGH1, 79 °C, whereas, chimera showed 78 °C. The improved structural integrity, thermostability and enhanced bi-functional enzyme activities of chimera makes it potentially useful for industrial application in converting biomass to glucose and thus bioethanol.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India
| | - Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sumitha Banu Jamaldheen
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vijayanand Suryakant Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Bashirova A, Pramanik S, Volkov P, Rozhkova A, Nemashkalov V, Zorov I, Gusakov A, Sinitsyn A, Schwaneberg U, Davari MD. Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability. Int J Mol Sci 2019; 20:E1602. [PMID: 30935060 PMCID: PMC6479618 DOI: 10.3390/ijms20071602] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/29/2023] Open
Abstract
Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15⁻21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52⁻58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15⁻22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
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Affiliation(s)
- Anna Bashirova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| | - Pavel Volkov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Vitaly Nemashkalov
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142292, Moscow region, Russia.
| | - Ivan Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexander Gusakov
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Arkady Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstrasse 50, Aachen 52056, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
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Coniglio RO, Fonseca MI, Díaz GV, Ontañon O, Ghio S, Campos E, Zapata PD. Optimization of cellobiohydrolase production and secretome analysis of Trametes villosa LBM 033 suitable for lignocellulosic bioconversion. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2019. [DOI: 10.1080/25765299.2019.1598107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Romina O. Coniglio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - María I. Fonseca
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Gabriela V. Díaz
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Ornella Ontañon
- Laboratorio de Bioenergía, Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Silvina Ghio
- Laboratorio de Bioenergía, Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Eleonora Campos
- Laboratorio de Bioenergía, Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Pedro D. Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
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30
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Hua C, Li W, Han W, Wang Q, Bi P, Han C, Zhu L. Characterization of a novel thermostable GH7 endoglucanase from Chaetomium thermophilum capable of xylan hydrolysis. Int J Biol Macromol 2018; 117:342-349. [DOI: 10.1016/j.ijbiomac.2018.05.189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/01/2018] [Accepted: 05/25/2018] [Indexed: 01/19/2023]
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31
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Functional characterization of GH7 endo-1,4-β-glucanase from Aspergillus fumigatus and its potential industrial application. Protein Expr Purif 2018; 150:1-11. [DOI: 10.1016/j.pep.2018.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/23/2022]
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32
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Bandara YMAY, Weerasooriya DK, Liu S, Little CR. The Necrotrophic Fungus Macrophomina phaseolina Promotes Charcoal Rot Susceptibility in Grain Sorghum Through Induced Host Cell-Wall-Degrading Enzymes. PHYTOPATHOLOGY 2018; 108:948-956. [PMID: 29465007 DOI: 10.1094/phyto-12-17-0404-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The cell-wall-degrading enzymes (CWDE) secreted by necrotrophs are important virulence factors. Although not unequivocally demonstrated, it has been suggested that necrotrophs induce hosts to cooperate in disease development through manipulation of host CWDE. The necrotrophic fungus Macrophomina phaseolina causes charcoal rot disease in Sorghum bicolor. An RNA-seq experiment was conducted to investigate the behavior of sorghum CWDE-encoding genes after M. phaseolina inoculation. Results revealed M. phaseolina's ability to significantly upregulate pectin methylesterase-, polygalacturonase-, cellulase-, endoglucanase-, and glycosyl hydrolase-encoding genes in a charcoal rot-susceptible sorghum genotype (Tx7000) but not in a resistant genotype (SC599). For functional validation, crude enzyme mixtures were extracted from M. phaseolina- and mock-inoculated charcoal-rot-resistant (SC599 and SC35) and -susceptible (Tx7000 and BTx3042) sorghum genotype stalks. A gel diffusion assay (pectin substrate) revealed significantly increased pectin methylesterase activity in M. phaseolina-inoculated Tx7000 and BTx3042. Polygalacturonase activity was determined using a ruthenium red absorbance assay (535 nm). Significantly increased polygalacturonase activity was observed in two susceptible genotypes after M. phaseolina inoculation. The activity of cellulose-degrading enzymes was determined using a 2-cyanoacetamide fluorimetric assay (excitation and emission maxima at 331 and 383 nm, respectively). The assay revealed significantly increased cellulose-degrading enzyme activity in M. phaseolina-inoculated Tx7000 and BTx3042. These findings revealed M. phaseolina's ability to promote charcoal rot susceptibility in grain sorghum through induced host CWDE.
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Affiliation(s)
- Y M A Y Bandara
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - D K Weerasooriya
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - S Liu
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
| | - C R Little
- First third, and fourth authors: Department of Plant Pathology, and second author: Department of Agronomy, Kansas State University, Manhattan 66506
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Engineering the conserved and noncatalytic residues of a thermostable β-1,4-endoglucanase to improve specific activity and thermostability. Sci Rep 2018; 8:2954. [PMID: 29440674 PMCID: PMC5811441 DOI: 10.1038/s41598-018-21246-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/01/2018] [Indexed: 12/18/2022] Open
Abstract
Endoglucanases are increasingly applied in agricultural and industrial applications as a key biocatalyst for cellulose biodegradation. However, the low performance in extreme conditions seriously challenges the enzyme’s commercial utilization. To obtain endoglucanases with substantially improved activity and thermostability, structure-based rational design was carried out based on the Chaetomium thermophilum β-1,4-endoglucanase CTendo45. In this study, five mutant enzymes were constructed by substitution of conserved and noncatalytic residues using site-directed mutagenesis. Mutants were constitutively expressed in Pichia pastoris, purified, and ultimately tested for enzymatic characteristics. Two single mutants, Y30F and Y173F, increased the enzyme’s specific activity 1.35- and 1.87-fold using carboxymethylcellulose sodium (CMC-Na) as a substrate, respectively. Furthermore, CTendo45 and mutants exhibited higher activity towards β-D-glucan than that of CMC-Na, and activities of Y173F and Y30F were also increased obviously against β-D-glucan. In addition, Y173F significantly improved the enzyme’s heat resistance at 80 °C and 90 °C. More interestingly, the double mutant Y30F/Y173F obtained considerably higher stability at elevated temperatures but failed to inherit the increased catalytic efficiency of its single mutant counterparts. This work gives an initial insight into the biological function of conserved and noncatalytic residues of thermostable endoglucanases and proposes a feasible path for the improvement of enzyme redesign proposals.
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34
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Preparation and characterization of the spherical nanosized cellulose by the enzymatic hydrolysis of pulp fibers. Carbohydr Polym 2018; 181:879-884. [DOI: 10.1016/j.carbpol.2017.11.064] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022]
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35
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Khalili Ghadikolaei K, Gharechahi J, Haghbeen K, Akbari Noghabi K, Hosseini Salekdeh G, Shahbani Zahiri H. A cold-adapted endoglucanase from camel rumen with high catalytic activity at moderate and low temperatures: an anomaly of truly cold-adapted evolution in a mesophilic environment. Extremophiles 2018; 22:315-326. [PMID: 29330650 DOI: 10.1007/s00792-018-0999-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/23/2017] [Indexed: 11/25/2022]
Abstract
Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3). The maximum activity of the enzyme on carboxymethyl cellulose (CMC) was obtained at pH 5 and 30 °C with a Vmax and Km of 339 U/mg and 2.57 mg/ml, respectively. The enzyme with an estimated low melting temperature of 45 °C and about 50% activity at 4 °C was identified to be cold-adapted. A thermodynamic analysis corroborated that CelCM3 with an activation energy (Ea), enthalpy of activation (ΔH), and Gibb's free energy (ΔG) of, respectively, 18.47 kJ mol-1, 16.12 kJ mol-1, and 56.09 kJ mol-1 is a cold-active endoglucanase. In addition, CelCM3 was tolerant of metal ions, non-ionic detergents, urea, and organic solvents. Given these interesting characteristics, CelCM3 shows promise to meet the requirements of industrial applications.
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Affiliation(s)
- Kamran Khalili Ghadikolaei
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kamahldin Haghbeen
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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36
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Chahed H, Boumaiza M, Ezzine A, Marzouki M. Heterologous expression and biochemical characterization of a novel thermostable Sclerotinia sclerotiorum GH45 endoglucanase in Pichia pastoris. Int J Biol Macromol 2018; 106:629-635. [DOI: 10.1016/j.ijbiomac.2017.08.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
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37
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Production of thermostable β-glucosidase and CMCase by Penicillium sp. LMI01 isolated from the Amazon region. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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38
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Operational Strategies for Enzymatic Hydrolysis in a Biorefinery. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2018. [DOI: 10.1007/978-3-319-67678-4_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Song EG, Ryu KH. A pepper mottle virus-based vector enables systemic expression of endoglucanase D in non-transgenic plants. Arch Virol 2017; 162:3717-3726. [PMID: 28864903 DOI: 10.1007/s00705-017-3539-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/02/2017] [Indexed: 12/16/2022]
Abstract
Plant-virus-based expression vectors have been used as an alternative to the creation of transgenic plants. Using a virus-based vector, we investigated the feasibility of producing the endoglucanase D (EngD) from Clostridium cellulovorans in Nicotiana benthamiana. This protein has endoglucanase, xylanase, and exoglucanase activities and may be of value for cellulose digestion in the generation of biofuels from plant biomass. The EngD gene was cloned between the nuclear inclusion b (NIb)- and coat protein (CP)-encoding sequences of pSP6PepMoV-Vb1. In vitro transcripts derived from the clone (pSP6PepMoV-Vb1/EngD) were infectious in N. benthamiana but caused milder symptoms than wild-type PepMoV-Vb1. RT-PCR amplification of total RNA from non-inoculated upper leaves infected with PepMoV-Vb1/EngD produced the target band for the CP, partial NIb and EngD-CP regions of PepMoV-V1/EngD, in addition to nonspecific bands. Western blot analysis showed the CP target bands of PepMoV-Vb1/EngD as well as non-target bands. EngD enzymatic activity in infected plants was detected using a glucose assay. The plant leaves showed increased senescence compared with healthy and PepMoV-Vb1-infected plants. Our study suggests the feasibility of using a viral vector for systemic infection of plants for expression of heterologous engD for the purpose of digesting a cellulose substrate in plant cells for biomass production.
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Affiliation(s)
- Eun Gyeong Song
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Seoul, Republic of Korea
| | - Ki Hyun Ryu
- Plant Virus GenBank, Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Seoul, Republic of Korea.
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40
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Meleiro LP, Carli S, Fonseca-Maldonado R, da Silva Torricillas M, Zimbardi ALRL, Ward RJ, Jorge JA, Furriel RPM. Overexpression of a Cellobiose-Glucose-Halotolerant Endoglucanase from Scytalidium thermophilum. Appl Biochem Biotechnol 2017; 185:316-333. [PMID: 29150773 DOI: 10.1007/s12010-017-2660-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/13/2017] [Indexed: 11/28/2022]
Abstract
Enzyme reaction products and by-products from pretreatment steps can inhibit endoglucanases and are major factors limiting the efficiency of enzymatic lignocellulosic biomass hydrolysis. The gene encoding the endoglucanase from Scytalidium thermophilum (egst) was cloned and expressed as a soluble protein in Pichia pastoris GS115. The recombinant enzyme (Egst) was monomeric (66 kDa) and showed an estimated carbohydrate content of 53.3% (w/w). The optimum temperature and pH of catalysis were 60-70 °C and pH of 5.5, respectively. The enzyme was highly stable at pH 3.0-8.0 with a half-life in water of 100 min at 65 °C. The Egst presented good halotolerance, retaining 84.1 and 71.4% of the control activity in the presence of 0.5 and 2.0 mol L-1 NaCl, respectively. Hydrolysis of medium viscosity carboxymethylcellulose (CMC) by Egst was stimulated 1.77-, 1.84-, 1.64-, and 1.8-fold by dithiothreitol, β-mercaptoethanol, cysteine, and manganese at 10, 10, 10, and 5 mmol L-1 concentration, respectively. The enzyme hydrolyzed CMC with maximal velocity and an apparent affinity constant of 432.10 ± 16.76 and 10.5 ± 2.53 mg mL-1, respectively. Furthermore, the Egst was tolerant to reaction products and able to act on pretreated fractions sugarcane bagasse demonstrating excellent properties for application in the hydrolysis of lignocellulosic biomass.
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Affiliation(s)
- Luana Parras Meleiro
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Sibeli Carli
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Marcela da Silva Torricillas
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ana Lucia Ribeiro Latorre Zimbardi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Richard John Ward
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Atílio Jorge
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rosa Prazeres Melo Furriel
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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41
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De Los Santos H, Hurley JM, Collins EJ, Bennett KP. Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2017; 2017:455-463. [PMID: 31844846 PMCID: PMC6913202 DOI: 10.1145/3107411.3107420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Circadian rhythms are endogenous cycles of approximately 24 hours reinforced by external cues such as light. These cycles are typically modeled as harmonic oscillators with fixed amplitude peaks. Using experimental data measuring global gene transcription in Neurospora crassa over 48 hours in the dark (i.e. with external queues removed), we demonstrate that many circadian genes frequently exhibit either damped harmonic oscillations, in which the peak amplitudes decrease each day, or driven harmonic oscillations, in which the peak amplitudes increase each day. By fitting extended harmonic oscillator models which include a damping ratio coefficient, we detected additional circadian genes that were not identified by the current standard tools that use fixed amplitude waves as reference, e.g. JTK_CYCLE. Functional Catalogue analysis confirms that our identified damped or driven genes exhibit distinct biological functions. The application of extended damped/driven harmonic oscillator models thus can elucidate, not only previously unidentified circadian genes, but also characterize gene subsets with expression patterns of biological relevance. Thus, expanded harmonic oscillators provide a powerful new tool for circadian system biology.
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Affiliation(s)
- Hannah De Los Santos
- Rensselaer Polytechnic Institute Institute for Data Exploration and Applications/Department of Mathematical Sciences Troy, NY 12180
| | - Jennifer M Hurley
- Rensselaer Polytechnic Institute Department of Biological Sciences/Center for Biotechnology and Interdisciplinary Sciences Troy, NY 12180
| | - Emily J Collins
- Rensselaer Polytechnic Institute Department of Biological Sciences/Center for Biotechnology and Interdisciplinary Sciences Troy, NY 12180
| | - Kristin P Bennett
- Rensselaer Polytechnic Institute Institute for Data Exploration and Applications/Department of Mathematical Sciences Troy, NY 12180
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42
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Takenaka M, Kobayashi T, Inokuma K, Hasunuma T, Maruyama T, Ogino C, Kondo A. Mapping of endoglucanases displayed on yeast cell surface using atomic force microscopy. Colloids Surf B Biointerfaces 2017; 151:134-142. [PMID: 27988474 DOI: 10.1016/j.colsurfb.2016.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/14/2016] [Accepted: 12/09/2016] [Indexed: 11/29/2022]
Abstract
The surface of yeast cells has been an attractive interface for the effective use of cellulose. Surface enzymes, however, are difficult to visualize and evaluate. In this study, two kinds of unique anchoring regions were used to display the cellulase, endoglucanase (EG), on a yeast cell surface. Differences in the display level and the localization of EG were observed by atomic force microscopy. By surveying the yeast cell surface with a chemically modified cantilever, the interactive force between the cellulose and EG was measured. Force curve mapping revealed differences in the display levels and the localization of EG according to anchoring regions. The proposed methodology enables visualization of displayed enzymes such as EG on the yeast cell surface.
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Affiliation(s)
- Musashi Takenaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takuya Kobayashi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tatsuo Maruyama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Haq IU, Akram F. Enhanced Production of a Recombinant Multidomain Thermostable GH9 Processive Endo-1,4-β-Glucanase (CenC) from Ruminiclostridium thermocellum in a Mesophilic Host Through Various Cultivation and Induction Strategies. Appl Biochem Biotechnol 2017; 183:171-188. [PMID: 28247309 DOI: 10.1007/s12010-017-2437-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/10/2017] [Indexed: 01/09/2023]
Abstract
Commonly, unintentional induction and inadvertently preparing medium for engineered Escherichia coli BL21 CodonPlus (DE3)-RIPL, give poor or variable yields of heterologous proteins. Therefore, to enhance the activity and production of an industrially relevant recombinant processive endo-1,4-β-glucanase (CenC) propagated in Escherichia coli BL21 CodonPlus(DE3)-RIPL through various cultivation and induction strategies. Investigation of various growth media and induction parameters revealed that high-cell-density and optimal CenC expression were obtained in ZYBM9 medium induced either with 0.5 mM IPTG/150 mM lactose, after 6 h induction at 37 °C; and before induction, bacterial cells were given heat shock (42 °C) for 1 h when culture density (OD600nm) reached at 0.6. Intracellular enzyme activity was enhanced by 6.67 and 3.20-fold in ZYBM9 and 3×ZYBM9 medium, respectively, under optimal conditions. Using YNG auto-induction medium, activity was 2.5-fold increased after 10 h incubation at 37 °C. Approximately similar results were obtained by transferring the optimized process at the bioreactor level. Results showed that the effective process strategy is essential to enhance recombinant bacterial cell mass and enzyme production from small to large-scale. To the best of our knowledge, this is the first ever report on enhanced production of thermostable processive endo-1,4-β-glucanase cloned from Ruminiclostridium thermocellum, which is a suitable candidate for industrial applications. Graphical Abstract Flow Chart Summary of Enhanced Production of a Recombinant Multidomain Thermostable GH9 Processive Endo-1,4-β-glucanase from Ruminiclostridium thermocellum.
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Affiliation(s)
- Ikram Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, -54000, Pakistan
| | - Fatima Akram
- Institute of Industrial Biotechnology, GC University, Lahore, -54000, Pakistan.
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Ledesma-Amaro R, Nicaud JM. Metabolic Engineering for Expanding the Substrate Range of Yarrowia lipolytica. Trends Biotechnol 2016; 34:798-809. [DOI: 10.1016/j.tibtech.2016.04.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
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45
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Moraïs S, Stern J, Kahn A, Galanopoulou AP, Yoav S, Shamshoum M, Smith MA, Hatzinikolaou DG, Arnold FH, Bayer EA. Enhancement of cellulosome-mediated deconstruction of cellulose by improving enzyme thermostability. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:164. [PMID: 27493686 PMCID: PMC4973527 DOI: 10.1186/s13068-016-0577-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 07/27/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND The concerted action of three complementary cellulases from Clostridium thermocellum, engineered to be stable at elevated temperatures, was examined on a cellulosic substrate and compared to that of the wild-type enzymes. Exoglucanase Cel48S and endoglucanase Cel8A, both key elements of the natural cellulosome from this bacterium, were engineered previously for increased thermostability, either by SCHEMA, a structure-guided, site-directed protein recombination method, or by consensus-guided mutagenesis combined with random mutagenesis using error-prone PCR, respectively. A thermostable β-glucosidase BglA mutant was also selected from a library generated by error-prone PCR that will assist the two cellulases in their methodic deconstruction of crystalline cellulose. The effects of a thermostable scaffoldin versus those of a largely mesophilic scaffoldin were also examined. By improving the stability of the enzyme subunits and the structural component, we aimed to improve cellulosome-mediated deconstruction of cellulosic substrates. RESULTS The results demonstrate that the combination of thermostable enzymes as free enzymes and a thermostable scaffoldin was more active on the cellulosic substrate than the wild-type enzymes. Significantly, "thermostable" designer cellulosomes exhibited a 1.7-fold enhancement in cellulose degradation compared to the action of conventional designer cellulosomes that contain the respective wild-type enzymes. For designer cellulosome formats, the use of the thermostabilized scaffoldin proved critical for enhanced enzymatic performance under conditions of high temperatures. CONCLUSIONS Simple improvement in the activity of a given enzyme does not guarantee its suitability for use in an enzyme cocktail or as a designer cellulosome component. The true merit of improvement resides in its ultimate contribution to synergistic action, which can only be determined experimentally. The relevance of the mutated thermostable enzymes employed in this study as components in multienzyme systems has thus been confirmed using designer cellulosome technology. Enzyme integration via a thermostable scaffoldin is critical to the ultimate stability of the complex at higher temperatures. Engineering of thermostable cellulases and additional lignocellulosic enzymes may prove a determinant parameter for development of state-of-the-art designer cellulosomes for their employment in the conversion of cellulosic biomass to soluble sugars.Graphical abstractConversion of conventional designer cellulosomes into thermophilic designer cellulosomes.
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Affiliation(s)
- Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Anastasia P. Galanopoulou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Shahar Yoav
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
- Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12, 76100 Rehovot, Israel
| | - Melina Shamshoum
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Matthew A. Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Dimitris G. Hatzinikolaou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
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Kim SJ, Joo JE, Jeon SD, Hyeon JE, Kim SW, Um YS, Han SO. Enhanced thermostability of mesophilic endoglucanase Z with a high catalytic activity at active temperatures. Int J Biol Macromol 2016; 86:269-76. [DOI: 10.1016/j.ijbiomac.2016.01.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 12/18/2022]
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Polarity Alteration of a Calcium Site Induces a Hydrophobic Interaction Network and Enhances Cel9A Endoglucanase Thermostability. Appl Environ Microbiol 2016; 82:1662-1674. [PMID: 26729722 DOI: 10.1128/aem.03326-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
Structural calcium sites control protein thermostability and activity by stabilizing native folds and changing local conformations. Alicyclobacillus acidocaldarius survives in thermal-acidic conditions and produces an endoglucanase Cel9A (AaCel9A) which contains a calcium-binding site (Ser465 to Val470) near the catalytic cleft. By superimposing the Ca(2+)-free and Ca(2+)-bounded conformations of the calcium site, we found that Ca(2+) induces hydrophobic interactions between the calcium site and its nearby region by driving a conformational change. The hydrophobic interactions at the high-B-factor region could be enhanced further by replacing the surrounding polar residues with hydrophobic residues to affect enzyme thermostability and activity. Therefore, the calcium-binding residue Asp468 (whose side chain directly ligates Ca(2+)), Asp469, and Asp471 of AaCel9A were separately replaced by alanine and valine. Mutants D468A and D468V showed increased activity compared with those of the wild type with 0 mM or 10 mM Ca(2+) added, whereas the Asp469 or Asp471 substitution resulted in decreased activity. The D468A crystal structure revealed that mutation D468A triggered a conformational change similar to that induced by Ca(2+) in the wild type and developed a hydrophobic interaction network between the calcium site and the neighboring hydrophobic region (Ala113 to Ala117). Mutations D468V and D468A increased 4.5°C and 5.9°C, respectively, in melting temperature, and enzyme half-life at 75°C increased approximately 13 times. Structural comparisons between AaCel9A and other endoglucanases of the GH9 family suggested that the stability of the regions corresponding to the AaCel9A calcium site plays an important role in GH9 endoglucanase catalysis at high temperature.
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48
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Improved stability and reusability of endoglucanase from Clostridium thermocellum by a biosilica-based auto-encapsulation method. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Wang Y, Yu W, Han F. Expression and characterization of a cold-adapted, thermotolerant and denaturant-stable GH5 endoglucanase Celal_2753 that withstands boiling from the psychrophilic bacterium Cellulophaga algicola IC166(T). Biotechnol Lett 2015; 38:285-90. [PMID: 26463370 DOI: 10.1007/s10529-015-1971-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/30/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To characterize a novel endoglucanase, Celal_2753, from the psychrophilic bacterium Cellulophaga algicola IC166(T). RESULTS Celal_2753 was purified to homogeneity with a yield of 81 % and with a molecular weight of 40 kDa on SDS-PAGE. It had maximum hydrolytic activity towards carboxymethyl cellulose at 40 °C and pH 6. It showed 33 % of the maximum activity at 10 ºC. Its activity increased to 272-316 % in the presence of 0.25-2 M NaCl and KCl at 40 °C. Celal_2753 was stable in the presence of 10 % (v/v) Tween 20, 10 % (v/v) Triton X-100, 16 mM SDS, 6 M urea or 2 M guanidine hydrochloride. Celal_2753 that had been boiled for 5 min recovered 55 % of its initial activity by incubating at 30 °C for 60 min. CONCLUSION Because of its cold-adapted, thermotolerant and denaturant-stable properties, endoglucanase Celal_2753 is promising in detergent industry and bioethanol production.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao, 266003, China.,Shandong Provincial Key Laboratory of Glycoscience & Glycotechnology, 5 Yushan Road, Qingdao, 266003, China.,School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao, 266003, China.,Shandong Provincial Key Laboratory of Glycoscience & Glycotechnology, 5 Yushan Road, Qingdao, 266003, China.,School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Feng Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao, 266003, China. .,Shandong Provincial Key Laboratory of Glycoscience & Glycotechnology, 5 Yushan Road, Qingdao, 266003, China. .,School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
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50
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CenC, a multidomain thermostable GH9 processive endoglucanase from Clostridium thermocellum: cloning, characterization and saccharification studies. World J Microbiol Biotechnol 2015; 31:1699-710. [DOI: 10.1007/s11274-015-1920-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/03/2015] [Indexed: 01/29/2023]
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